סמינר מחלקתי- הנדסה ביו רפואית

אסף ליברמן

תלמיד התואר השלישי במחלקה להנדסה ביו רפואית

אוניברסיטת תל אביב

Cell Studio: a platform for real-time, interactive 3D Graphical simulation of immunological processes

In the core of systems biology are computer models, which integrate static experimental ‘omics’ data into dynamic representations of the researched biological system. These representations are then simulated - run on a computer – to promote understanding of the system. The field of computer modeling and simulation of biological systems is rapidly advancing, with many simulation systems created in the past 20 years. It is backed by significant progress in the fields of experimentation techniques, computer hardware and programming software. The result of a simulation may be delivered in several ways, from numerical results, through graphs of the simulated run, to a visualization of the simulation. The vision of an in-silico experiment viewed as if it was undertaken in reality under a microscope is appealing, but technically demanding and computationally-intensive. We use game engines - generic programs for game creation that offer ready-made assets and tools - to create a visualized, interactive simulation. We also utilize a scalable architecture that delegates the computational load into a scalable server. Together, these may aid in overcoming technical challenges.

Here we report “Cell Studio”, a generic, hybrid platform to simulate an immune microenvironment with biological and biophysical rules. The simulation may be visualized in interactive real-time 3D: The user may view the simulation, move the ‘camera’ around, stop, fast-forward and rewind it, and inject soluble molecules into the extracellular medium at any point in time. During simulation, graphs are created in real time for a broad view of system wide processes. The model is parametrized using a user-friendly Graphical User Interface (GUI). We believe that real-time, interactive 3D visualization may improve insight generated from the simulation, and encourage intuition about emergent behavior in the modelled biological system.

העבודה נעשתה בהנחיית ד"ר אורי נבו מהמחלקה להנדסה ביו-רפואית,  אוניברסיטת תל-אביב

ההרצאה תתקיים ביום ראשון 23.04.17, בשעה 14:30

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב